Figure 3.

(A) Stereo representation of the tetrahedral intermediate in the reaction to acyl-enzyme through direct Lys47 protonation. Hydrogen bonds are shown as dashed lines (distances in Å between heteroatoms). The tetrahedral species is nestled between β₉ sheet and the loop connecting α₄ and α₅ helices, with the protein depicted as the ribbon representation in green. Important active site residues and the tetrahedral intermediate are represented in capped-stick. Carbon atoms are colored in gray, nitrogen in blue, oxygen in red, and hydrogen in cyan. Distances (Å) are rounded to the nearest tenth. (B) QM/MM potential-energy surface and the contour over reaction coordinates represented as a shadow. The reaction paths are shown by red and green arrows from the tetrahedral intermediate (I) to an intermediate complex (II), and to the acyl-enzyme (III). The energy surface constructed using the complex coordinates (d₃–d_NH) vs d₄ is qualitatively identical. The distance d_NH is the distance between the lysine NH atoms. (C) The structure of the acyl-enzyme III is shown. The general description given for panel A applies here as well.